DNA sequences from the nuclear gene waxy were used to assess phylogenetic relationships within Jaltomata, a group of approximately 60 species from Central and South America. Phylogenetic analyses identify two primary groups: a morphologically diverse group from western South America, characterized by orange fruits, and a primarily Mesoamerican clade with black/purple fruit and little morphological diversity. We also identify an early-diverging lineage of Jaltomata species with red fruits, which is sister to the rest of the genus. Ancestral character state reconstruction supports a view of the common ancestor of the genus originating in South America and having rotate corollas similar to many species of Solanum. In addition, we infer independent colonizations of lomas habitats by Jaltomata species and show a correlation between red nectar production and campanulate floral form in multiple lineages, suggesting a common evolutionary syndrome related to pollination.